## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(shannonaov)
## W = 0.9291, p-value = 0.5732
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 1.0859, df = 1, p-value = 0.2974
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.0527 0.0527 0.15 0.718
## Residuals 4 1.4061 0.3515
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = shannondata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 -0.1874213 -1.531512 1.15667 0.7183604
##
##
## --------------------------------------------------------------
## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(simpsonaov)
## W = 0.88738, p-value = 0.3047
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 0.74903, df = 1, p-value = 0.3868
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.0052 0.00519 0.059 0.82
## Residuals 4 0.3506 0.08764
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = simpsondata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 -0.05883652 -0.7299494 0.6122763 0.8196598
##
##
## --------------------------------------------------------------
## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(richaov)
## W = 0.93289, p-value = 0.6026
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 3.2991, df = 1, p-value = 0.06932
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 7.288 7.288 1.561 0.28
## Residuals 4 18.670 4.667
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = richdata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 2.204189 -2.693449 7.101827 0.2795884
##
##
## --------------------------------------------------------------
##
## Call:
## adonis(formula = bray.distance ~ data5$treatment)
##
## Permutation: free
## Number of permutations: 719
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## data5$treatment 1 1.01309 1.01309 4.6942 0.53992 0.1
## Residuals 4 0.86326 0.21582 0.46008
## Total 5 1.87635 1.00000
## Run 0 stress 4.35166e-05
## Run 1 stress 9.206128e-05
## ... Procrustes: rmse 0.2192141 max resid 0.4447335
## Run 2 stress 0
## ... New best solution
## ... Procrustes: rmse 0.1475603 max resid 0.2719593
## Run 3 stress 0.1967694
## Run 4 stress 0
## ... Procrustes: rmse 0.1503594 max resid 0.2805032
## Run 5 stress 0
## ... Procrustes: rmse 0.1890022 max resid 0.2367295
## Run 6 stress 0
## ... Procrustes: rmse 0.1525354 max resid 0.2259206
## Run 7 stress 0
## ... Procrustes: rmse 0.1446005 max resid 0.2074821
## Run 8 stress 0
## ... Procrustes: rmse 0.132074 max resid 0.2500861
## Run 9 stress 0
## ... Procrustes: rmse 0.1888654 max resid 0.3103119
## Run 10 stress 0
## ... Procrustes: rmse 0.1321098 max resid 0.2335853
## Run 11 stress 0
## ... Procrustes: rmse 0.1086904 max resid 0.198957
## Run 12 stress 0
## ... Procrustes: rmse 0.184796 max resid 0.2895882
## Run 13 stress 0
## ... Procrustes: rmse 0.1985743 max resid 0.2828424
## Run 14 stress 0
## ... Procrustes: rmse 0.1839276 max resid 0.339448
## Run 15 stress 0
## ... Procrustes: rmse 0.1569956 max resid 0.2738898
## Run 16 stress 0
## ... Procrustes: rmse 0.08147595 max resid 0.1293814
## Run 17 stress 0
## ... Procrustes: rmse 0.1231843 max resid 0.1929613
## Run 18 stress 0
## ... Procrustes: rmse 0.2154224 max resid 0.3725087
## Run 19 stress 0
## ... Procrustes: rmse 0.09658586 max resid 0.169947
## Run 20 stress 0
## ... Procrustes: rmse 0.1123304 max resid 0.1810664
## Run 21 stress 0
## ... Procrustes: rmse 0.07114148 max resid 0.08562701
## Run 22 stress 0
## ... Procrustes: rmse 0.1207696 max resid 0.2088403
## Run 23 stress 0
## ... Procrustes: rmse 0.1338395 max resid 0.2011499
## Run 24 stress 0
## ... Procrustes: rmse 0.2011198 max resid 0.2879716
## Run 25 stress 7.960692e-05
## ... Procrustes: rmse 0.1835879 max resid 0.3361377
## Run 26 stress 7.465245e-05
## ... Procrustes: rmse 0.1516833 max resid 0.21161
## Run 27 stress 4.134366e-05
## ... Procrustes: rmse 0.158652 max resid 0.1955455
## Run 28 stress 9.401493e-05
## ... Procrustes: rmse 0.1705531 max resid 0.3146807
## Run 29 stress 0
## ... Procrustes: rmse 0.140281 max resid 0.1899751
## Run 30 stress 0
## ... Procrustes: rmse 0.1569951 max resid 0.237474
## Run 31 stress 0
## ... Procrustes: rmse 0.21383 max resid 0.3404873
## Run 32 stress 0
## ... Procrustes: rmse 0.1831665 max resid 0.2903409
## Run 33 stress 0
## ... Procrustes: rmse 0.1862874 max resid 0.2430944
## Run 34 stress 0
## ... Procrustes: rmse 0.1398732 max resid 0.194408
## Run 35 stress 0
## ... Procrustes: rmse 0.08385465 max resid 0.1208572
## Run 36 stress 0
## ... Procrustes: rmse 0.1531769 max resid 0.2654934
## Run 37 stress 0.1420473
## Run 38 stress 0
## ... Procrustes: rmse 0.168821 max resid 0.2760271
## Run 39 stress 0
## ... Procrustes: rmse 0.2398039 max resid 0.4101748
## Run 40 stress 4.958545e-05
## ... Procrustes: rmse 0.1690092 max resid 0.224612
## Run 41 stress 0
## ... Procrustes: rmse 0.1763536 max resid 0.2979007
## Run 42 stress 8.50985e-05
## ... Procrustes: rmse 0.2037257 max resid 0.3652396
## Run 43 stress 0
## ... Procrustes: rmse 0.1373896 max resid 0.1978843
## Run 44 stress 0
## ... Procrustes: rmse 0.1721457 max resid 0.2384637
## Run 45 stress 8.338233e-06
## ... Procrustes: rmse 0.1350539 max resid 0.1826055
## Run 46 stress 8.733644e-05
## ... Procrustes: rmse 0.1864883 max resid 0.2843063
## Run 47 stress 0
## ... Procrustes: rmse 0.1287125 max resid 0.1800035
## Run 48 stress 1.294414e-05
## ... Procrustes: rmse 0.06488975 max resid 0.09540012
## Run 49 stress 0
## ... Procrustes: rmse 0.1123794 max resid 0.2193415
## Run 50 stress 0
## ... Procrustes: rmse 0.0873931 max resid 0.1388494
## Run 51 stress 0
## ... Procrustes: rmse 0.1836172 max resid 0.2892836
## Run 52 stress 0
## ... Procrustes: rmse 0.1349277 max resid 0.2496178
## Run 53 stress 0
## ... Procrustes: rmse 0.1597566 max resid 0.3010393
## Run 54 stress 0
## ... Procrustes: rmse 0.1578135 max resid 0.2739341
## Run 55 stress 0.1420473
## Run 56 stress 9.580941e-05
## ... Procrustes: rmse 0.2385671 max resid 0.3099702
## Run 57 stress 0
## ... Procrustes: rmse 0.1424363 max resid 0.203378
## Run 58 stress 0
## ... Procrustes: rmse 0.1498625 max resid 0.2312135
## Run 59 stress 0
## ... Procrustes: rmse 0.08465851 max resid 0.1346232
## Run 60 stress 0
## ... Procrustes: rmse 0.1430299 max resid 0.2610707
## Run 61 stress 0
## ... Procrustes: rmse 0.1369128 max resid 0.1816959
## Run 62 stress 0
## ... Procrustes: rmse 0.08119163 max resid 0.1444967
## Run 63 stress 0
## ... Procrustes: rmse 0.1710694 max resid 0.240634
## Run 64 stress 9.84601e-05
## ... Procrustes: rmse 0.1878078 max resid 0.2714905
## Run 65 stress 0
## ... Procrustes: rmse 0.05651144 max resid 0.09672819
## Run 66 stress 8.62831e-05
## ... Procrustes: rmse 0.0727498 max resid 0.09722458
## Run 67 stress 0
## ... Procrustes: rmse 0.1958305 max resid 0.2910121
## Run 68 stress 2.701363e-05
## ... Procrustes: rmse 0.2225825 max resid 0.3507306
## Run 69 stress 7.042554e-05
## ... Procrustes: rmse 0.173566 max resid 0.2626667
## Run 70 stress 2.745518e-05
## ... Procrustes: rmse 0.08284383 max resid 0.124135
## Run 71 stress 0
## ... Procrustes: rmse 0.1840454 max resid 0.3503948
## Run 72 stress 0
## ... Procrustes: rmse 0.1540941 max resid 0.2302387
## Run 73 stress 0
## ... Procrustes: rmse 0.07616243 max resid 0.1113843
## Run 74 stress 0
## ... Procrustes: rmse 0.1348955 max resid 0.2398141
## Run 75 stress 0
## ... Procrustes: rmse 0.1593818 max resid 0.2624199
## Run 76 stress 0
## ... Procrustes: rmse 0.1658679 max resid 0.2368498
## Run 77 stress 0
## ... Procrustes: rmse 0.1083634 max resid 0.1355875
## Run 78 stress 0
## ... Procrustes: rmse 0.173316 max resid 0.2188972
## Run 79 stress 2.412692e-05
## ... Procrustes: rmse 0.1513869 max resid 0.2559945
## Run 80 stress 0
## ... Procrustes: rmse 0.1286293 max resid 0.1708846
## Run 81 stress 8.249084e-05
## ... Procrustes: rmse 0.1600543 max resid 0.2790534
## Run 82 stress 0
## ... Procrustes: rmse 0.06425533 max resid 0.09782641
## Run 83 stress 0
## ... Procrustes: rmse 0.1859754 max resid 0.3306764
## Run 84 stress 1.218079e-05
## ... Procrustes: rmse 0.1579732 max resid 0.2679705
## Run 85 stress 0
## ... Procrustes: rmse 0.1373995 max resid 0.1704452
## Run 86 stress 0
## ... Procrustes: rmse 0.1135352 max resid 0.1456319
## Run 87 stress 3.345478e-06
## ... Procrustes: rmse 0.1136627 max resid 0.1526098
## Run 88 stress 7.30298e-05
## ... Procrustes: rmse 0.09087387 max resid 0.1523526
## Run 89 stress 0
## ... Procrustes: rmse 0.1294085 max resid 0.20968
## Run 90 stress 0
## ... Procrustes: rmse 0.2133609 max resid 0.307295
## Run 91 stress 0
## ... Procrustes: rmse 0.208796 max resid 0.3331994
## *** No convergence -- monoMDS stopping criteria:
## 88: stress < smin
## 1: stress ratio > sratmax
## 2: scale factor of the gradient < sfgrmin
## [1] "No Convergence"
## Run 0 stress 9.179259e-05
## Run 1 stress 0
## ... New best solution
## ... Procrustes: rmse 0.1912644 max resid 0.3064663
## Run 2 stress 0
## ... Procrustes: rmse 0.1515697 max resid 0.1940969
## Run 3 stress 8.011522e-05
## ... Procrustes: rmse 0.2408658 max resid 0.3233412
## Run 4 stress 0
## ... Procrustes: rmse 0.1502567 max resid 0.2373834
## Run 5 stress 0
## ... Procrustes: rmse 0.1824273 max resid 0.2309358
## Run 6 stress 0
## ... Procrustes: rmse 0.2044446 max resid 0.3064849
## Run 7 stress 0
## ... Procrustes: rmse 0.1360824 max resid 0.1868316
## Run 8 stress 0
## ... Procrustes: rmse 0.224697 max resid 0.3889081
## Run 9 stress 1.601269e-06
## ... Procrustes: rmse 0.2017323 max resid 0.253622
## Run 10 stress 0
## ... Procrustes: rmse 0.2332277 max resid 0.2830118
## Run 11 stress 0
## ... Procrustes: rmse 0.2094351 max resid 0.3393129
## Run 12 stress 0
## ... Procrustes: rmse 0.1924744 max resid 0.2476726
## Run 13 stress 0
## ... Procrustes: rmse 0.1723438 max resid 0.2779048
## Run 14 stress 0
## ... Procrustes: rmse 0.231938 max resid 0.3082758
## Run 15 stress 0
## ... Procrustes: rmse 0.1591339 max resid 0.2941593
## Run 16 stress 1.844663e-05
## ... Procrustes: rmse 0.1367305 max resid 0.1893536
## Run 17 stress 0
## ... Procrustes: rmse 0.2432104 max resid 0.3742779
## Run 18 stress 0
## ... Procrustes: rmse 0.2021536 max resid 0.3190184
## Run 19 stress 8.261138e-05
## ... Procrustes: rmse 0.2661264 max resid 0.3395278
## Run 20 stress 0
## ... Procrustes: rmse 0.2050021 max resid 0.3470228
## Run 21 stress 0
## ... Procrustes: rmse 0.2349675 max resid 0.3899205
## Run 22 stress 0
## ... Procrustes: rmse 0.1743172 max resid 0.3327414
## Run 23 stress 0
## ... Procrustes: rmse 0.1805854 max resid 0.2484891
## Run 24 stress 0
## ... Procrustes: rmse 0.2214565 max resid 0.3735158
## Run 25 stress 6.602248e-05
## ... Procrustes: rmse 0.2633094 max resid 0.3328158
## Run 26 stress 0
## ... Procrustes: rmse 0.1989565 max resid 0.3402747
## Run 27 stress 0
## ... Procrustes: rmse 0.2434265 max resid 0.2853429
## Run 28 stress 0
## ... Procrustes: rmse 0.1437204 max resid 0.2008141
## Run 29 stress 0
## ... Procrustes: rmse 0.2207409 max resid 0.2922027
## Run 30 stress 0
## ... Procrustes: rmse 0.140996 max resid 0.2320052
## Run 31 stress 0
## ... Procrustes: rmse 0.1889331 max resid 0.2900138
## Run 32 stress 0
## ... Procrustes: rmse 0.1834047 max resid 0.2422162
## Run 33 stress 0
## ... Procrustes: rmse 0.2447367 max resid 0.3580808
## Run 34 stress 0
## ... Procrustes: rmse 0.2359379 max resid 0.3172238
## Run 35 stress 0
## ... Procrustes: rmse 0.2428633 max resid 0.3027342
## Run 36 stress 0
## ... Procrustes: rmse 0.2011346 max resid 0.344021
## Run 37 stress 0
## ... Procrustes: rmse 0.2398276 max resid 0.4186627
## Run 38 stress 6.012963e-05
## ... Procrustes: rmse 0.2290966 max resid 0.3002383
## Run 39 stress 0
## ... Procrustes: rmse 0.2681661 max resid 0.4893852
## Run 40 stress 2.102041e-05
## ... Procrustes: rmse 0.1696101 max resid 0.2438495
## Run 41 stress 0
## ... Procrustes: rmse 0.2461656 max resid 0.3874782
## Run 42 stress 8.813298e-05
## ... Procrustes: rmse 0.2458929 max resid 0.3572947
## Run 43 stress 1.301719e-06
## ... Procrustes: rmse 0.196147 max resid 0.322213
## Run 44 stress 0
## ... Procrustes: rmse 0.1521486 max resid 0.2327491
## Run 45 stress 7.430631e-05
## ... Procrustes: rmse 0.2806763 max resid 0.3795962
## Run 46 stress 0
## ... Procrustes: rmse 0.1268192 max resid 0.1828082
## Run 47 stress 0
## ... Procrustes: rmse 0.1656652 max resid 0.2345423
## Run 48 stress 0
## ... Procrustes: rmse 0.2071554 max resid 0.3748716
## Run 49 stress 8.899945e-05
## ... Procrustes: rmse 0.2411995 max resid 0.3239697
## Run 50 stress 8.49387e-05
## ... Procrustes: rmse 0.2235364 max resid 0.2957555
## Run 51 stress 8.946254e-05
## ... Procrustes: rmse 0.2411916 max resid 0.3239556
## Run 52 stress 0
## ... Procrustes: rmse 0.1024931 max resid 0.1772733
## Run 53 stress 0
## ... Procrustes: rmse 0.1805318 max resid 0.2266111
## Run 54 stress 0
## ... Procrustes: rmse 0.222073 max resid 0.3309312
## Run 55 stress 0
## ... Procrustes: rmse 0.1984136 max resid 0.2676206
## Run 56 stress 4.061045e-05
## ... Procrustes: rmse 0.1650274 max resid 0.2850801
## Run 57 stress 0
## ... Procrustes: rmse 0.2278851 max resid 0.350922
## Run 58 stress 0
## ... Procrustes: rmse 0.1401086 max resid 0.185101
## Run 59 stress 8.737338e-05
## ... Procrustes: rmse 0.2411935 max resid 0.3239583
## Run 60 stress 0
## ... Procrustes: rmse 0.2191345 max resid 0.3940798
## Run 61 stress 2.198444e-05
## ... Procrustes: rmse 0.2350082 max resid 0.3891647
## Run 62 stress 0
## ... Procrustes: rmse 0.2048775 max resid 0.265205
## Run 63 stress 0
## ... Procrustes: rmse 0.2213181 max resid 0.3503163
## Run 64 stress 0
## ... Procrustes: rmse 0.1501829 max resid 0.2294057
## Run 65 stress 0
## ... Procrustes: rmse 0.1411666 max resid 0.2546569
## Run 66 stress 0
## ... Procrustes: rmse 0.1464234 max resid 0.2116882
## Run 67 stress 0
## ... Procrustes: rmse 0.1652729 max resid 0.2477694
## Run 68 stress 9.870175e-05
## ... Procrustes: rmse 0.2505968 max resid 0.3328449
## Run 69 stress 0.07976986
## Run 70 stress 0
## ... Procrustes: rmse 0.194331 max resid 0.2432624
## Run 71 stress 6.941015e-05
## ... Procrustes: rmse 0.2130009 max resid 0.3004891
## Run 72 stress 7.615578e-05
## ... Procrustes: rmse 0.259831 max resid 0.34112
## Run 73 stress 0
## ... Procrustes: rmse 0.1647591 max resid 0.2388743
## Run 74 stress 0
## ... Procrustes: rmse 0.1644595 max resid 0.2847747
## Run 75 stress 0
## ... Procrustes: rmse 0.1906808 max resid 0.3100185
## Run 76 stress 0
## ... Procrustes: rmse 0.146477 max resid 0.2315368
## Run 77 stress 7.361458e-05
## ... Procrustes: rmse 0.2474006 max resid 0.3599023
## Run 78 stress 0
## ... Procrustes: rmse 0.1476474 max resid 0.2302322
## Run 79 stress 0
## ... Procrustes: rmse 0.1500008 max resid 0.1972427
## Run 80 stress 0
## ... Procrustes: rmse 0.2317812 max resid 0.3787597
## Run 81 stress 0
## ... Procrustes: rmse 0.2462261 max resid 0.3285394
## Run 82 stress 0
## ... Procrustes: rmse 0.1343457 max resid 0.1992015
## Run 83 stress 0
## ... Procrustes: rmse 0.1171339 max resid 0.2019657
## Run 84 stress 0
## ... Procrustes: rmse 0.1754114 max resid 0.255796
## Run 85 stress 0
## ... Procrustes: rmse 0.17915 max resid 0.2562237
## Run 86 stress 0
## ... Procrustes: rmse 0.2158695 max resid 0.2893261
## Run 87 stress 0
## ... Procrustes: rmse 0.1897326 max resid 0.3018936
## Run 88 stress 8.264709e-05
## ... Procrustes: rmse 0.2704232 max resid 0.3402092
## Run 89 stress 0
## ... Procrustes: rmse 0.1770887 max resid 0.2768628
## Run 90 stress 7.124833e-05
## ... Procrustes: rmse 0.2274275 max resid 0.3037865
## Run 91 stress 0
## ... Procrustes: rmse 0.2291196 max resid 0.3758455
## *** No convergence -- monoMDS stopping criteria:
## 90: stress < smin
## 1: stress ratio > sratmax
## [1] "No Convergence"